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Miscellaneous software for laboratory work

Here are some small utilities I wrote to make life easier in the lab. They are here mainly for the benefit of the biochemistry people at UW Chemistry, but anyone who happens to have use for them may help themselves. No liability.

SpectraAnalysis.xla

This is an Add-In for MS Excel, for the processing and analysis of fluorescence and absorbance spectra. It can import the following file formats:

  • Text files exported by the PTI FeliX32 software running the QuantaMaster instrument in ESC 238A. (Make sure you specify "*.txt", not "*.spc" or "*.ang" as the file extension when saving the data).
  • Text files ("*.wsx") files, generated by the wavescan software that may at some time be installed to run the Ultrospec spectrophotometer, presently in C2-360.
  • *.SPT files, generated by the ancient DM3000F software that is found on older SPEX machines.

Further file formats could be added. If you need some new format, give me an email with some example files attached. If the format is binary, not text, please also provide some file format specification. ('Binary' applies if you see garbage if you open the file with a text editor.)

Instructions for installation

  1. Download the two files, SpectraAnalysis.xls and SpectraAnalysis.xla, into the same directory on your computer.
  2. Open Excel. From the 'Tools' menu, choose 'Add-Ins', 'Browse'. Navigate to SpectraAnalysis.xla and click on it. This will install three meenu options 'Spectra: Something' into your 'Tools' menu.
  3. If you want to upgrade to a more recent version (if there is one, check the file date...), just replace SpectraAnalysis.xls.

Instructions for use

Try and see. Some help is provided in the program. If you get stuck, give me an email.

DataPicker.xla

This is a small Add-In for MS Excel that helps with the extraction of selected data from large worksheets. I wrote it to manage the files generated by the Molecular Kinetics reader; however, it can be used with arbitrary files.

Instructions for installation

  1. Download the file DataPicker.xla to your computer.
  2. Open Excel. From the 'Tools' menu, choose 'Add-Ins', 'Browse'. Navigate to the downloaded file and select it. This will install the menu option 'Data Picker' into your 'Tools' menu.

Instructions for use

To use it with Molecular Kinetics files,

  1. export your data from the reader program as text files.
  2. Open them with Excel and accept the defaults (delimited, tabs as separators) proposed by Excel.
  3. Select some cells, call Data Picker from the Tools menu, and try it out. Some help is provided in the program.
ms_eps2csv

This is a really wonky thing - MassLynx displays spectra as graphs and extracts all the peaks but seems to be unable to export graphs that is displays in any generic file format. This program is a workaround - it extracts the data points from the graphics printed to a postscript file and saves them to a csv file, which can be imported into Excel or other spreadsheets.

Note that this only extracts the graph itself but no annotation, e.g. no peaks and so on. Also, the numerical accuracy is limited by the resolution of the 'printed' graph. The purpose of this thing really is only to get the graph into some editable format that you can tweak for display in other programs. For data analysis, use MassLynx.

Instructions for installation

In Richard's lab at UW, this program is already set up for you.

If not at UW: Download the zip file and unpack it some convenient location. Open the folder that was extracted and create a link on the Desktop to ms_eps2csv.exe.

You probably also want to set up a printer driver for easily creating the postscript files from MassLynx. Instructions on the setup procedure can be found here.

Instructions for use

Open the program, load the postscript file created from MassLynx, and save to csv. Only display one graph at a time in MassLynx, or ms_eps2csv will upchuck.